Read the Docs build information Build id: 27842 Project: dssc-operation-manual Version: latest Commit: de3bddcfa142ba236ebc72b0f92be1ee3a89fb15 Date: 2024-03-19T19:37:33.357508Z State: finished Success: True [rtd-command-info] start-time: 2024-03-19T19:37:37.786969Z, end-time: 2024-03-19T19:37:38.588187Z, duration: 0, exit-code: 0 git clone --no-single-branch --depth 50 http://git.xfel.eu/detectors/dssc_documentation.git . Cloning into '.'... [rtd-command-info] start-time: 2024-03-19T19:37:38.876497Z, end-time: 2024-03-19T19:37:38.980665Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at de3bddc Update new gain files. https://in.xfel.eu/elog/DSSC+1+Mpix+Detector/700 [rtd-command-info] start-time: 2024-03-19T19:37:39.070329Z, end-time: 2024-03-19T19:37:39.135360Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-03-19T19:37:40.481997Z, end-time: 2024-03-19T19:37:45.644988Z, duration: 5, exit-code: 0 python3.7 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/python3.7 Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2024-03-19T19:37:45.737397Z, end-time: 2024-03-19T19:37:46.743319Z, duration: 1, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/lib/python3.7/site-packages (24.0) [rtd-command-info] start-time: 2024-03-19T19:37:46.828132Z, end-time: 2024-03-19T19:37:56.415558Z, duration: 9, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/python -m pip install --upgrade --no-cache-dir jinja2==2.11.3 markupsafe==2.0.1 Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting jinja2==2.11.3 Downloading Jinja2-2.11.3-py2.py3-none-any.whl.metadata 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readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Attempting uninstall: setuptools Found existing installation: setuptools 68.0.0 Uninstalling setuptools-68.0.0: Successfully uninstalled setuptools-68.0.0 Successfully installed Pygments-2.3.1 alabaster-0.7.13 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 commonmark-0.8.1 docutils-0.14 future-1.0.0 idna-3.6 imagesize-1.4.1 jinja2-2.11.3 markupsafe-2.0.1 mock-1.0.1 packaging-24.0 pillow-5.4.1 pytz-2024.1 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.31.0 setuptools-41.0.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.7 [rtd-command-info] start-time: 2024-03-19T19:37:56.504980Z, end-time: 2024-03-19T19:37:59.851376Z, duration: 3, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Collecting git+https://git.xfel.eu/xfel-rtd/rtd-conf.git (from -r requirements.txt (line 3)) Cloning https://git.xfel.eu/xfel-rtd/rtd-conf.git to /tmp/pip-req-build-ky7_qjq2 Running command git clone --filter=blob:none --quiet https://git.xfel.eu/xfel-rtd/rtd-conf.git /tmp/pip-req-build-ky7_qjq2 Resolved https://git.xfel.eu/xfel-rtd/rtd-conf.git to commit 3d66246db37045eaa716d206b13441613c1b413e Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: sphinx in /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 4)) (1.8.6) Collecting breathe==4.7.3 (from -r requirements.txt (line 5)) Downloading breathe-4.7.3-py2.py3-none-any.whl.metadata (1.0 kB) Collecting slumber==0.7.1 (from -r requirements.txt (line 6)) Downloading slumber-0.7.1.tar.gz (10 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): 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duration: 0, exit-code: 0 cat source/conf.py #!/usr/bin/env python3.8.3 # -*- coding: utf-8 -*- # # pnCCD documentation build configuration file, created by # sphinx-quickstart on Tuesday January 28, 2020 at 11:25:48. # # This file is execfile()d with the current directory set to its # containing directory. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.graphviz', 'sphinx.ext.autosectionlabel', ] # Ensure that autosectionlabel will produce unique names autosectionlabel_prefix_document = True autosectionlabel_maxdepth = 4 # Add any paths that contain templates here, relative to this directory. templates_path = ['.templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The encoding of source files. # # source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = 'DSSC' copyright = '2020, XFEL Detector Operation Group' #author = 'XFEL Detector Group' author = u'David Lomidze, Monica Turcato' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = '1.0' # The full version, including alpha/beta/rc tags. release = ': Version 1.0' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: # # today = '' # # Else, today_fmt is used as the format for a strftime call. # # today_fmt = '%B %d, %Y' # If True, figures, tables and code-blocks are automatically numbered if they # have a caption. The numref role is enabled. Obeyed so far only by HTML and # LaTeX builders. Default is False. numfig = True # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This patterns also effect to html_static_path and html_extra_path exclude_patterns = [] # The reST default role (used for this markup: `text`) to use for all # documents. # # default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. # # add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). # # add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. # # show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. # modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. # keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = True # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom themes here, relative to this directory. # html_theme_path = [] # The name for this set of Sphinx documents. # " v documentation" by default. # html_title = 'The DSSC Detector Operation Manual' # A shorter title for the navigation bar. Default is the same as html_title. # html_short_title = "DSSC Manual" # The name of an image file (relative to this directory) to place at the top # of the sidebar. # # html_logo = None # The name of an image file (relative to this directory) to use as a favicon of # the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. # # html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". #html_static_path = ['.static'] html_static_path = ['_static'] # ['_static'] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. # # html_extra_path = [] # If not None, a 'Last updated on:' timestamp is inserted at every page # bottom, using the given strftime format. # The empty string is equivalent to '%b %d, %Y'. # # html_last_updated_fmt = None # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. # # html_use_smartypants = True # Custom sidebar templates, maps document names to template names. # # html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. # # html_additional_pages = {} # If false, no module index is generated. # # html_domain_indices = True # If false, no index is generated. # # html_use_index = True # If true, the index is split into individual pages for each letter. # # html_split_index = False # If true, links to the reST sources are added to the pages. # # html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. # # html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. # # html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. # # html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). # html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'h', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'r', 'sv', 'tr', 'zh' # # html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # 'ja' uses this config value. # 'zh' user can custom change `jieba` dictionary path. # # html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. # # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. htmlhelp_basename = 'DSSCdoc' # -- Options for LaTeX output --------------------------------------------- latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # #'preamble': # To get rid of blank pages after each chapter: 'extraclassoptions': 'openany,oneside,dvipsnames', 'preamble': r'''\newcommand{\docutilsrolemybold}{\bfseries} \newcommand{\DUrolered}[1]{{\color{Red}#1}} \newcommand{\DUroleblue}[1]{{\color{Blue}#1}} \newcommand{\DUrolegreen}[1]{{\color{Green}#1}} \newcommand{\DUroleyellow}[1]{{\color{Yellow}#1}} ''' # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). #latex_documents = [ # (master_doc, 'pnCCD.tex', 'pnCCD Documentation', # 'XFEL Detector Group', 'manual'), #] latex_documents = [ (master_doc, 'DSSC.tex', 'The DSSC Operation Manual', 'David Lomidze, Monica Turcato', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. # # latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. # # latex_use_parts = False # If true, show page references after internal links. # # latex_show_pagerefs = False # If true, show URL addresses after external links. # # latex_show_urls = False # Documents to append as an appendix to all manuals. # # latex_appendices = [] # It false, will not define \strong, \code, itleref, \crossref ... but only # \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added # packages. # # latex_keep_old_macro_names = True # If false, no module index is generated. # # latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'dssc', 'The DSSC Operation Manual', [author], 1) ] # If true, show URL addresses after external links. # # man_show_urls = False # -- Options for Texinfo output ------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'DSSC', 'The DSSC Operation Manual', author, 'DSSC', 'This is the DSSC detector operation manual.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. # # texinfo_appendices = [] # If false, no module index is generated. # # texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. # # texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. # # texinfo_no_detailmenu = False # Example configuration for intersphinx: refer to the Python standard library. #intersphinx_mapping = {'https://docs.python.org/': None} #we add a custum function to work with intersphinx import slumber import json # the RTDHOST should be set to localhost if you only compile on RTD # otherwise it needs to be set to the server hosting the internal RTD RTDHOST = 'https://rtd.xfel.eu/' api = slumber.API(base_url='{}/api/v2/'.format(RTDHOST)) projects = api.project.get()['results'] isphinx = {'python': ('http://python.readthedocs.io/en/latest/', None), 'numpy': ('http://numpy.readthedocs.io/en/latest/', None), 'scipy': ('http://scipy.readthedocs.io/en/latest/', None)} for proj in projects: isphinx[proj['slug'].replace('-', '')] = \ ('{}/docs/{}/en/latest'.format(RTDHOST, proj['slug']), None) #intersphinx_mapping = isphinx intersphinx_mapping = {'https://docs.python.org/': None} def setup(app): app.add_config_value('includeDevInfo', 'false', 'env') ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import importlib import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'http://rtd.xfel.eu/websupport' websupport2_static_url = '/static/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "media/", 'STATIC_URL': "/static/", 'PRODUCTION_DOMAIN': "rtd.xfel.eu", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//rtd.xfel.eu/downloads/dssc-operation-manual/latest/pdf/"), ("html", "//rtd.xfel.eu/downloads/dssc-operation-manual/latest/htmlzip/"), ("epub", "//rtd.xfel.eu/downloads/dssc-operation-manual/latest/epub/"), ], 'subprojects': [ ], 'slug': 'dssc-operation-manual', 'name': u'DSSC Operation Manual', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'http://rtd.xfel.eu/docs/dssc-operation-manual/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/source/', 'api_host': 'http://rtd.xfel.eu', 'github_user': 'None', 'proxied_api_host': '/_', 'github_repo': 'None', 'github_version': 'master', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'None', 'commit': 'de3bddcf', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2024-03-19T19:38:00.784067Z, end-time: 2024-03-19T19:38:04.109107Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.6 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 16 source files that are out of date updating environment: 16 added, 0 changed, 0 removed reading sources... [ 6%] QuandantMotion reading sources... [ 12%] SCSExpertStartup reading sources... [ 18%] abstract reading sources... [ 25%] acronyms reading sources... [ 31%] configurationFilesSCS reading sources... [ 37%] configurationFilesSQS reading sources... [ 43%] daq reading sources... [ 50%] dsscConfigFileGeneration reading sources... [ 56%] index reading sources... [ 62%] miscellanea reading sources... [ 68%] powering reading sources... [ 75%] preface reading sources... [ 81%] revisions reading sources... [ 87%] shutdown reading sources... [ 93%] troubleshooting reading sources... [100%] vacuum_and_cooling /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/QuandantMotion.rst:15: WARNING: Title underline too short. Understanding Opening and Closing the aperture ********************************* /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/abstract.rst:1: WARNING: Content block expected for the "raw" directive; none found. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/daq.rst:21: WARNING: Bullet list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/dsscConfigFileGeneration.rst:5: WARNING: Title underline too short. Environment Setup ---------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:17: WARNING: Unexpected section title. Miscellanea =========== /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:20: WARNING: Unexpected section title. Connecting to the online cluster -------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:25: WARNING: Unexpected section title. Setting up the DSSC processor viewer ------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:52: WARNING: Unexpected section title. Detector synchronization ------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:72: WARNING: Unexpected section title. DSSC manual powering up procedure: Switching ON the in-vacuum electronics up to ASICs ------------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:103: WARNING: Unexpected section title. Configuring the detector ASICs ------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:108: WARNING: Unexpected section title. Manual procedure: powering up the source voltages and the high voltage channels ------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:127: WARNING: Unexpected section title. Manual procedure: powering off the DSSC detector ------------------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:: WARNING: image file not readable: Figures/figure5.4.png /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/powering.rst:82: WARNING: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:99: WARNING: Malformed table. +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:97: WARNING: Error parsing content block for the "table" directive: exactly one table expected. .. table:: Data taking issues +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 6%] QuandantMotion writing output... [ 12%] SCSExpertStartup writing output... [ 18%] abstract writing output... [ 25%] acronyms writing output... [ 31%] configurationFilesSCS writing output... [ 37%] configurationFilesSQS writing output... [ 43%] daq writing output... 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[rtd-command-info] start-time: 2024-03-19T19:38:04.444210Z, end-time: 2024-03-19T19:38:07.718813Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.6 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 16 added, 0 changed, 0 removed reading sources... [ 6%] QuandantMotion reading sources... [ 12%] SCSExpertStartup reading sources... [ 18%] abstract reading sources... [ 25%] acronyms reading sources... 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Understanding Opening and Closing the aperture ********************************* /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/abstract.rst:1: WARNING: Content block expected for the "raw" directive; none found. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/daq.rst:21: WARNING: Bullet list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/dsscConfigFileGeneration.rst:5: WARNING: Title underline too short. Environment Setup ---------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:17: WARNING: Unexpected section title. Miscellanea =========== /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:20: WARNING: Unexpected section title. Connecting to the online cluster -------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:25: WARNING: Unexpected section title. Setting up the DSSC processor viewer ------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:52: WARNING: Unexpected section title. Detector synchronization ------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:72: WARNING: Unexpected section title. DSSC manual powering up procedure: Switching ON the in-vacuum electronics up to ASICs ------------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:103: WARNING: Unexpected section title. Configuring the detector ASICs ------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:108: WARNING: Unexpected section title. Manual procedure: powering up the source voltages and the high voltage channels ------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:127: WARNING: Unexpected section title. Manual procedure: powering off the DSSC detector ------------------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:: WARNING: image file not readable: Figures/figure5.4.png /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/powering.rst:82: WARNING: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:99: WARNING: Malformed table. +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:97: WARNING: Error parsing content block for the "table" directive: exactly one table expected. .. table:: Data taking issues +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done assembling single document... revisions abstract preface acronyms vacuum_and_cooling powering daq QuandantMotion shutdown miscellanea troubleshooting configurationFilesSCS configurationFilesSQS dsscConfigFileGeneration SCSExpertStartup /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:105: WARNING: undefined label: config writing... /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/index.rst:11: WARNING: toctree contains reference to document 'preface' that doesn't have a title: no link will be generated /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/index.rst:11: WARNING: toctree contains reference to document 'acronyms' that doesn't have a title: no link will be generated /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/index.rst:11: WARNING: toctree contains reference to document 'miscellanea' that doesn't have a title: no link will be generated done writing additional files... copying images... 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[rtd-command-info] start-time: 2024-03-19T19:38:07.855527Z, end-time: 2024-03-19T19:38:11.041719Z, duration: 3, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/envs/latest/bin/sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.8.6 loading translations [en]... done making output directory... loading intersphinx inventory from https://docs.python.org/objects.inv... intersphinx inventory has moved: https://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 16 added, 0 changed, 0 removed reading sources... [ 6%] QuandantMotion reading sources... [ 12%] SCSExpertStartup reading sources... [ 18%] abstract reading sources... [ 25%] acronyms reading sources... [ 31%] configurationFilesSCS reading sources... [ 37%] configurationFilesSQS reading sources... 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Understanding Opening and Closing the aperture ********************************* /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/abstract.rst:1: WARNING: Content block expected for the "raw" directive; none found. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/daq.rst:21: WARNING: Bullet list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/dsscConfigFileGeneration.rst:5: WARNING: Title underline too short. Environment Setup ---------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:17: WARNING: Unexpected section title. Miscellanea =========== /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:20: WARNING: Unexpected section title. Connecting to the online cluster -------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:25: WARNING: Unexpected section title. Setting up the DSSC processor viewer ------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:52: WARNING: Unexpected section title. Detector synchronization ------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:72: WARNING: Unexpected section title. DSSC manual powering up procedure: Switching ON the in-vacuum electronics up to ASICs ------------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:103: WARNING: Unexpected section title. Configuring the detector ASICs ------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:108: WARNING: Unexpected section title. Manual procedure: powering up the source voltages and the high voltage channels ------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:127: WARNING: Unexpected section title. Manual procedure: powering off the DSSC detector ------------------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:: WARNING: image file not readable: Figures/figure5.4.png /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/powering.rst:82: WARNING: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:99: WARNING: Malformed table. +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:97: WARNING: Error parsing content block for the "table" directive: exactly one table expected. .. table:: Data taking issues +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ looking for now-outdated files... none found pickling environment... done checking consistency... done processing DSSC.tex...index revisions abstract preface acronyms vacuum_and_cooling powering daq QuandantMotion shutdown miscellanea troubleshooting configurationFilesSCS configurationFilesSQS dsscConfigFileGeneration SCSExpertStartup resolving references... /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:105: WARNING: undefined label: config writing... done copying images... 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[100%] Figures/fig1_chapter6.png copying TeX support files... done build succeeded, 17 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2024-03-19T19:38:13.577117Z, end-time: 2024-03-19T19:38:13.639748Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2024-03-19T19:38:13.728294Z, end-time: 2024-03-19T19:38:19.934763Z, duration: 6, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=dssc-operation-manual -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="dssc-operation-manual" "DSSC.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on dssc-operation-manual.pdf (47 pages, 3123165 bytes). Transcript written on dssc-operation-manual.log. Latexmk: Index file 'dssc-operation-manual.idx' was written Latexmk: Missing input file: 'dssc-operation-manual.ind' from line 'No file dssc-operation-manual.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'dssc-operation-manual.pdf' Latexmk: List of undefined refs and citations: Reference `QuandantMotion:dsscmotionsystem' on page 22 undefined on input line 716 Reference `QuandantMotion:dsscmotionsystem' on page 22 undefined on input line 766 Reference `QuandantMotion:motionlogfile' on page 25 undefined on input line 793 Reference `QuandantMotion:motionsteps' on page 22 undefined on input line 728 Reference `daq:chapter3' on page 10 undefined on input line 484 Reference `daq:daq' on page 17 undefined on input line 537 Reference `daq:dssccontrol' on page 17 undefined on input line 603 Reference `daq:metadata' on page 19 undefined on input line 612 Reference `powering:configuring' on page 8 undefined on input line 368 Reference `powering:figure10' on page 14 undefined on input line 495 Reference `powering:figure3' on page 7 undefined on input line 279 Reference `powering:figure4' on page 7 undefined on input line 295 Reference `powering:figure5' on page 7 undefined on input line 296 Reference `powering:figure6' on page 8 undefined on input line 395 Reference `powering:figure7' on page 10 undefined on input line 411 Reference `powering:figure7' on page 28 undefined on input line 953 Reference `powering:figure8' on page 10 undefined on input line 446 Reference `powering:mpod-ips' on page 14 undefined on input line 516 Reference `powering:powering' on page 8 undefined on input line 371 Reference `powering:switchingon' on page 8 undefined on input line 365 Reference `shutdown:figure12' on page 28 undefined on input line 953 Reference `vacuum_and_cooling:figure1' on page 4 undefined on input line 237 Reference `vacuum_and_cooling:figure2' on page 4 undefined on input line 253 Latexmk: Summary of warnings: Latex failed to resolve 25 reference(s) Rule 'makeindex dssc-operation-manual.idx': File changes, etc: Non-existent destination files: 'dssc-operation-manual.ind' ------------ Run number 1 of rule 'makeindex dssc-operation-manual.idx' ------------ ------------ Running 'makeindex -s python.ist -o "dssc-operation-manual.ind" "dssc-operation-manual.idx"' ------------ Latexmk: applying rule 'makeindex dssc-operation-manual.idx'... 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(./dssc-operation-manual.toc Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 31. [1]) [2] Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 86. Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 86. Package Fancyhdr Warning: \fancyhead's `E' option without twoside option is use less on input line 86. Chapter 1. Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 140. [1] Chapter 2. Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 146. [2] [3] Chapter 3. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 255. [4] [5 <./DSSC_Main.png>] [6 <./SIB.png>] Chapter 4. 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[40] [41] Chapter 11. Underfull \hbox (badness 7759) in paragraph at lines 2458--2459 \T1/ptm/m/n/10 Create a folder in your of-fice PC \T1/pcr/m/n/10 mkdir dsscConf igFileGenerator \T1/ptm/m/n/10 go into the folder \T1/pcr/m/n/10 cd Overfull \hbox (42.25323pt too wide) in paragraph at lines 2491--2493 []\T1/pcr/m/n/10 dssccalibration/notebooks/GeneratePixelGainConfiguration. Overfull \vbox (1.80615pt too high) detected at line 2538 Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 2538. [42] [43] Chapter 12. Package Fancyhdr Warning: \fancyfoot's `E' option without twoside option is use less on input line 2597. [44] (./dssc-operation-manual.ind) [45] (./dssc-operation-manual.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrr8a.pfb> Output written on dssc-operation-manual.pdf (48 pages, 3130607 bytes). 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Understanding Opening and Closing the aperture ********************************* /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/abstract.rst:1: WARNING: Content block expected for the "raw" directive; none found. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/daq.rst:21: WARNING: Bullet list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/dsscConfigFileGeneration.rst:5: WARNING: Title underline too short. Environment Setup ---------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:17: WARNING: Unexpected section title. Miscellanea =========== /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:20: WARNING: Unexpected section title. Connecting to the online cluster -------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:25: WARNING: Unexpected section title. Setting up the DSSC processor viewer ------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:52: WARNING: Unexpected section title. Detector synchronization ------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:72: WARNING: Unexpected section title. DSSC manual powering up procedure: Switching ON the in-vacuum electronics up to ASICs ------------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:103: WARNING: Unexpected section title. Configuring the detector ASICs ------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:108: WARNING: Unexpected section title. Manual procedure: powering up the source voltages and the high voltage channels ------------------------------------------------------------------------------- /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:127: WARNING: Unexpected section title. Manual procedure: powering off the DSSC detector ------------------------------------------------ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:: WARNING: image file not readable: Figures/figure5.4.png /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/powering.rst:82: WARNING: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:99: WARNING: Malformed table. +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/troubleshooting.rst:97: WARNING: Error parsing content block for the "table" directive: exactly one table expected. .. table:: Data taking issues +---------------------------+---------------------------+------------------------------------------------------+ | Scene | Issue | Action | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | PPT devices in error state| Try shutting down the corresponding | | PPT/ASICs Configuration | | :code:`SCS_CDIDET_DSSC(SQS_NSQ_DSSC)/FPGA/PPT_Qi` devices and | | panels | | instantiate them again. If this does not work, call | | | | DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output rate is zero for | Check if data are sent from detector. Press start | | PPT/ASICs Configuration | all quadrants | data sending. | | panels | | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Output is zero for one | Open the Init Qi scene of the quadrant not sending | | PPT/ASICs Configuration | quadrant | the data. Press Init System and then RUN XFEL mode. | | panels | | If this does not work, call DET OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`DSSC_Main`/ | Start PPT devices button | Open the Init Qi scenes of the single quadrants and | | PPT/ASICs Configuration | has no effect (no change | press Init System in each of them. Then go back to | | panels | of currents as in | the PPT/ASICs Configuration panels and when the | | | :numref:`config` | currents are OK (see :numref:`config`), press Init | | | | PPT devices there. If this does not work, call DET | | | | OCD. | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ | :code:`PREVIEW_CORRECTED` | :code:`PREVIEW` not | See :numref:`Online` | | | updating | | +---------------------------+---------------------------+------------------------------------------------------+ looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 6%] QuandantMotion writing output... [ 12%] SCSExpertStartup writing output... [ 18%] abstract writing output... [ 25%] acronyms writing output... [ 31%] configurationFilesSCS writing output... [ 37%] configurationFilesSQS writing output... [ 43%] daq writing output... 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[100%] vacuum_and_cooling /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/index.rst:11: WARNING: toctree contains reference to document 'preface' that doesn't have a title: no link will be generated /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/index.rst:11: WARNING: toctree contains reference to document 'acronyms' that doesn't have a title: no link will be generated /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/index.rst:11: WARNING: toctree contains reference to document 'miscellanea' that doesn't have a title: no link will be generated /usr/src/app/checkouts/readthedocs.org/user_builds/dssc-operation-manual/checkouts/latest/source/miscellanea.rst:105: WARNING: undefined label: config generating indices... genindex writing additional pages... copying images... [ 4%] Figures/MotionCordSys.png copying images... [ 9%] Figures/MotionSteps.png copying images... [ 13%] Figures/DAQ_v2.png copying images... [ 18%] Figures/DSSC_CONTROL.png copying images... [ 22%] Figures/metaData.png copying images... [ 27%] Figures/SIB2.png copying images... [ 31%] Figures/Power.png copying images... [ 36%] Figures/HV.png copying images... [ 40%] Figures/AON.png copying images... [ 45%] Figures/Auto_Power.png copying images... [ 50%] Figures/PPT_ASICS.png copying images... [ 54%] Figures/Panel1.png copying images... [ 59%] Figures/Panel2.png copying images... [ 63%] Figures/IOB.png copying images... [ 68%] Figures/RB.png copying images... [ 72%] Figures/Preview.png copying images... [ 77%] Figures/ASICS.png copying images... [ 81%] Figures/ASICS_Map.png copying images... [ 86%] Figures/Fig12.png copying images... [ 90%] Figures/fig1_chapter6.png copying images... [ 95%] Figures/DSSC_Main.png copying images... [100%] Figures/SIB.png copying static files... done copying extra files... 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